3O6F

Crystal structure of a human autoimmune TCR MS2-3C8 bound to MHC class II self-ligand MBP/HLA-DR4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of a TCR with high affinity for self-antigen reveals basis for escape from negative selection.

Yin, Y.Li, Y.Kerzic, M.C.Martin, R.Mariuzza, R.A.

(2011) EMBO J 30: 1137-1148

  • DOI: 10.1038/emboj.2011.21
  • Primary Citation of Related Structures:  
    3O6F

  • PubMed Abstract: 
  • The failure to eliminate self-reactive T cells during negative selection is a prerequisite for autoimmunity. To escape deletion, autoreactive T-cell receptors (TCRs) may form unstable complexes with self-peptide-MHC by adopting suboptimal binding topologies compared with anti-microbial TCRs ...

    The failure to eliminate self-reactive T cells during negative selection is a prerequisite for autoimmunity. To escape deletion, autoreactive T-cell receptors (TCRs) may form unstable complexes with self-peptide-MHC by adopting suboptimal binding topologies compared with anti-microbial TCRs. Alternatively, escape can occur by weak binding between self-peptides and MHC. We determined the structure of a human autoimmune TCR (MS2-3C8) bound to a self-peptide from myelin basic protein (MBP) and the multiple sclerosis-associated MHC molecule HLA-DR4. MBP is loosely accommodated in the HLA-DR4-binding groove, accounting for its low affinity. Conversely, MS2-3C8 binds MBP-DR4 as tightly as the most avid anti-microbial TCRs. MS2-3C8 engages self-antigen via a docking mode that resembles the optimal topology of anti-foreign TCRs, but is distinct from that of other autoreactive TCRs. Combined with a unique CDR3β conformation, this docking mode compensates for the weak binding of MBP to HLA-DR4 by maximizing interactions between MS2-3C8 and MBP. Thus, the MS2-3C8-MBP-DR4 complex reveals the basis for an alternative strategy whereby autoreactive T cells escape negative selection, yet retain the ability to initiate autoimmunity.


    Organizational Affiliation

    Institute for Bioscience and Biotechnology Research, University of Maryland, WM Keck Laboratory for Structural Biology, Rockville, MD, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chainA, E182Homo sapiensMutation(s): 0 
Gene Names: HLA-DRAHLA-DRA1
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UniProt GroupP01903
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DRB1-4 beta chainB, F221Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell receptor alpha chain C regionC, G206Homo sapiensMutation(s): 0 
Gene Names: TRACTCRA
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PHAROS:  P01848
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UniProt GroupP01848
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell receptor beta-1 chain C regionD, H245Homo sapiensMutation(s): 1 
Gene Names: TRBC1
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UniProt GroupA0A5B9
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.48α = 90
b = 218.403β = 90
c = 98.412γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-09-07
    Changes: Database references
  • Version 1.3: 2017-08-09
    Changes: Advisory, Refinement description, Source and taxonomy